Teaching biology students data exploration and visualization in a data-driven world.

As biologists accumulate or encounter increasingly large and complex data sets, our field creates the need for students to develop skills in data exploration and visualization. Many biology courses lack the time for students to develop the skills needed to parse complex datasets and visualize them appropriately. We developed a new upper-level undergraduate biology course to focused on data exploration and communication without requiring previous coding experience.

R Markdown as a dynamic interface for teaching: Modules from math and biology classrooms.

Advancing technologies, including interactive tools, are changing classroom pedagogy across academia. Here, we discuss the R Markdown interface, which allows for the creation of partial or complete interactive classroom modules for courses using the R programming language. R Markdown files mix sections of R code with formatted text, including LaTeX, which are rendered together to form complete reports and documents.

Identification of Rifampicin Resistance Mutations in Escherichia coli, Including an Unusual Deletion Mutation.

Rifampicin is an effective antibiotic against mycobacterial and other bacterial infections, but resistance readily emerges in laboratory and clinical settings. We screened Escherichia coli for rifampicin resistance and identified numerous mutations to the gene encoding the β-chain of RNA polymerase (rpoB), including an unusual 9-nucleotide deletion mutation. Structural modeling of the deletion mutant indicates locations of potential steric clashes with rifampicin.

A beacon in the cytoplasm: Tracking translation of single mRNAs.

Translation is carefully regulated to control protein levels and allow quick responses to changes in the environment. Certain questions about translation in vivo have been unattainable until now. In this issue, Pichon et al.

Coupling between the DEAD-box RNA helicases Ded1p and eIF4A.

Eukaryotic translation initiation involves two conserved DEAD-box RNA helicases, eIF4A and Ded1p. Here we show that S. cerevisiae eIF4A and Ded1p directly interact with each other and simultaneously with the scaffolding protein eIF4G.

Packing them up and dusting them off: RNA helicases and mRNA storage.

Cytoplasmic mRNA can be translated, translationally repressed, localized or degraded. Regulation of translation is an important step in control of gene expression and the cell can change whether and to what extent an mRNA is translated. If an mRNA is not translating, it will associate with translation repression factors; the mRNA can be stored in these non-translating states.

Analysis of RNA helicases in P-bodies and stress granules.

Cytoplasmic mRNA protein complexes (mRNPs) can assemble in granules, such as processing bodies (P-bodies) and stress granules (SGs). Both P-bodies and SGs contain repressed messenger RNAs (mRNAs) and proteins that regulate the fate of the mRNA. P-bodies contain factors involved in translation repression and mRNA decay; SGs contain a subset of translation initiation factors and mRNA-binding proteins.

The DEAD-box protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex.

The translation, localization, and degradation of cytoplasmic mRNAs are controlled by the formation and rearrangement of their mRNPs. The conserved Ded1/DDX3 DEAD-box protein functions in an unknown manner to affect both translation initiation and repression. We demonstrate that Ded1 first functions by directly interacting with eIF4G to assemble a Ded1-mRNA-eIF4F complex, which accumulates in stress granules.

Stressed out? Make some modifications!

Stress granules and processing bodies are related mRNA-containing granules implicated in controlling mRNA translation and decay. A genomic screen identifies numerous factors affecting granule formation, including proteins involved in -GlcNAc modifications. These results highlight the importance of post-translational modifications in translational control and mRNP granule formation.

The DEAD-box RNA helicase Ded1p affects and accumulates in Saccharomyces cerevisiae P-bodies.

Recent results suggest that cytoplasmic mRNAs can form translationally repressed messenger ribonucleoprotein particles (mRNPs) capable of decapping and degradation, or accumulation into cytoplasmic processing bodies (P-bodies), which can function as sites of mRNA storage. The proteins that function in transitions between the translationally repressed mRNPs that accumulate in P-bodies and mRNPs engaged in translation are largely unknown. Herein, we demonstrate that the yeast translation initiation factor Ded1p can localize to P-bodies.

U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing.

To ligate exons in pre-messenger RNA (pre-mRNA) splicing, the spliceosome must reposition the substrate after cleaving the 5' splice site. Because spliceosomal small nuclear RNAs (snRNAs) bind the substrate, snRNA structures may rearrange to reposition the substrate. However, such rearrangements have remained undefined.

Multiple functions for the invariant AGC triad of U6 snRNA.

The invariant AGC triad of U6 snRNA plays an essential, unknown role in splicing. The triad has been implicated in base-pairing with residues in U2, U4, and U6. Through a genetic analysis in S.